BioC 3.3: CHECK report for RMassBank on oaxaca

Package: RMassBank

Version: 2.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RMassBank_2.0.0.tar.gz

StartedAt: 2016-05-17 06:21:18 -0700 (Tue, 17 May 2016)

EndedAt: 2016-05-17 06:24:26 -0700 (Tue, 17 May 2016)

EllapsedTime: 188.3 seconds

RetCode: 0

Status:  OK

CheckDir: RMassBank.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RMassBank_2.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/RMassBank.Rcheck’
* using R version 3.3.0 (2016-05-03)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RMassBank/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RMassBank’ version ‘2.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RMassBank’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.findPattern: no visible global function definition for
  ‘capture.output’
.get.mol2formula: no visible global function definition for
  ‘capture.output’
.pubChemOnline: no visible global function definition for ‘URLencode’
addPeaks: no visible global function definition for ‘read.csv’
analyzeMsMs.formula.optimized: no visible binding for global variable
  ‘occurrenceMatrix’
checkIsotopes: no visible global function definition for ‘data’
checkIsotopes : <anonymous> : <anonymous>: no visible global function
  definition for ‘points’
createSpecsFromPeaklists: no visible global function definition for
  ‘read.csv’
deprofile.spline : <anonymous>: no visible global function definition
  for ‘smooth.spline’
deprofile.spline : <anonymous>: no visible global function definition
  for ‘predict’
findEIC: no visible global function definition for ‘predict’
findMsMsHRperxcms.direct : getRT : <anonymous>: no visible global
  function definition for ‘median’
findMsMsHRperxcms.direct: no visible global function definition for
  ‘capture.output’
gatherSpectrum: no visible global function definition for
  ‘packageVersion’
getCSID: no visible global function definition for ‘URLencode’
getCactus: no visible global function definition for ‘URLencode’
getCtsKey: no visible global function definition for ‘URLencode’
getMolecule: no visible global function definition for ‘capture.output’
getPcCHEBI: no visible global function definition for ‘URLencode’
getPcIUPAC: no visible global function definition for ‘URLencode’
getPcId: no visible global function definition for ‘URLencode’
getPcInchiKey: no visible global function definition for ‘URLencode’
getPcSDF: no visible global function definition for ‘URLencode’
getPcSynonym: no visible global function definition for ‘URLencode’
loadInfolist: no visible global function definition for ‘read.csv’
loadInfolist: no visible global function definition for ‘read.csv2’
loadList: no visible global function definition for ‘read.csv’
loadList: no visible global function definition for ‘read.csv2’
makeMollist: no visible global function definition for ‘write.table’
makeRecalibration: no visible global function definition for ‘par’
mbWorkflow: no visible global function definition for ‘write.csv’
msmsRead: no visible global function definition for ‘read.csv’
msmsRead.RAW : getRT : <anonymous>: no visible global function
  definition for ‘median’
msmsRead.RAW: no visible global function definition for
  ‘capture.output’
msmsRead.ticms2: no visible global function definition for ‘read.csv’
msmsRead.ticms2: no visible global function definition for
  ‘c.msmsWSspecs’
newStep2WorkFlow: no visible global function definition for ‘read.csv’
parseMassBank: no visible binding for global variable ‘type.convert’
parseMassBank: no visible global function definition for
  ‘flush.console’
plotMbWorkspaces: no visible global function definition for ‘points’
plotRecalibration: no visible global function definition for ‘par’
plotRecalibration.direct: no visible global function definition for
  ‘predict’
plotRecalibration.direct: no visible global function definition for
  ‘lines’
plotRecalibration.direct: no visible global function definition for
  ‘heat.colors’
processProblematicPeaks: no visible global function definition for
  ‘write.csv’
progressBarHook: no visible global function definition for
  ‘txtProgressBar’
progressBarHook: no visible global function definition for
  ‘setTxtProgressBar’
recalibrate.identity: no visible global function definition for ‘lm’
recalibrate.linear: no visible global function definition for ‘lm’
recalibrate.loess: no visible global function definition for ‘loess’
recalibrate.mean: no visible global function definition for ‘lm’
recalibrateSingleSpec: no visible global function definition for
  ‘predict’
toRMB : <anonymous>: no visible global function definition for ‘median’
show,mbWorkspace: no visible global function definition for ‘str’
Undefined global functions or variables:
  URLencode c.msmsWSspecs capture.output data flush.console heat.colors
  lines lm loess median occurrenceMatrix packageVersion par points
  predict read.csv read.csv2 setTxtProgressBar smooth.spline str
  txtProgressBar type.convert write.csv write.table
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "lines", "par", "points")
  importFrom("stats", "lm", "loess", "median", "predict",
             "smooth.spline")
  importFrom("utils", "URLencode", "capture.output", "data",
             "flush.console", "packageVersion", "read.csv", "read.csv2",
             "setTxtProgressBar", "str", "txtProgressBar",
             "type.convert", "write.csv", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
getCactus 0.129  0.006   5.499
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/RMassBank.Rcheck/00check.log’
for details.

* installing *source* package ‘RMassBank’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RMassBank)

name	user	system	elapsed
CTS.externalIdSubset	0.001	0.000	0.000
CTS.externalIdTypes	0	0	0
RmbDefaultSettings	0.005	0.001	0.006
add.formula	0.005	0.000	0.005
addMB	0.001	0.000	0.000
addPeaks	0.001	0.000	0.000
addPeaksManually	0.001	0.000	0.001
aggregateSpectra	0.001	0.000	0.001
analyzeMsMs	0.001	0.001	0.001
annotator.default	0.001	0.000	0.000
archiveResults	0.011	0.000	0.011
cleanElnoise	0.001	0.000	0.001
combineMultiplicities	0.001	0.000	0.001
compileRecord	0.001	0.000	0.000
createMolfile	0.001	0.000	0.001
dbe	0.001	0.000	0.001
deprofile	0.001	0.000	0.001
exportMassbank	0.001	0.001	0.001
filterLowaccResults	0.000	0.000	0.001
filterMultiplicity	0	0	0
filterPeakSatellites	0.000	0.000	0.001
filterPeaksMultiplicity	0	0	0
findMass	0.747	0.030	0.546
findMsMsHR	0.001	0.000	0.001
findMsMsHRperxcms	0.001	0.000	0.000
findMz	0.000	0.000	0.001
findMz.formula	0.032	0.001	0.044
findProgress	0.003	0.000	0.001
flatten	0.001	0.000	0.001
formulastring.to.list	0.005	0.001	0.002
gatherCompound	0.000	0.000	0.001
gatherData	0.000	0.000	0.001
gatherDataBabel	0.000	0.001	0.001
gatherDataUnknown	0	0	0
gatherPubChem	0	0	0
getCSID	0	0	0
getCactus	0.129	0.006	5.499
getCtsKey	0.051	0.001	0.672
getCtsRecord	0.015	0.002	0.151
getMolecule	0.053	0.000	0.054
getPcId	0.075	0.002	1.322
is.valid.formula	0.001	0.000	0.001
loadInfolists	0.000	0.000	0.001
loadList	0.001	0.000	0.001
makeMollist	0.001	0.000	0.000
makeRecalibration	0.000	0.000	0.001
mbWorkflow	0	0	0
order.formula	0.002	0.000	0.002
parseMassBank	0	0	0
plotMbWorkspaces	0.001	0.000	0.001
ppm	0.001	0.000	0.000
problematicPeaks	0.000	0.001	0.001
reanalyzeFailpeaks	0	0	0
recalibrate	0.001	0.000	0.001
recalibrate.addMS1data	0	0	0
smiles2mass	0.000	0.000	0.001
to.limits.rcdk	0.002	0.000	0.002
toMassbank	0.000	0.000	0.001
toRMB	0.001	0.000	0.000
updateSettings	0.001	0.000	0.000
validate	0.000	0.001	0.000